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Detailed information for vg0413685186:

Variant ID: vg0413685186 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 13685186
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.19, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CTAGAGTTTTTGCCATGGCTGCTAGGTTTTCAACTAAGCCTCATGTTTTCGATGGAACTGATTTTTCTCATGGTGTAGTAGGATGCAATCTTACATTATG[A/G]
CTGAGGATTATGATATTCGGAGAAAAGTCAAATCCTTATGTGATTCCTGAACAAATTAATACTGCTCCTTTAAAAACTGAATTTGAACAAAATTACAAAG

Reverse complement sequence

CTTTGTAATTTTGTTCAAATTCAGTTTTTAAAGGAGCAGTATTAATTTGTTCAGGAATCACATAAGGATTTGACTTTTCTCCGAATATCATAATCCTCAG[T/C]
CATAATGTAAGATTGCATCCTACTACACCATGAGAAAAATCAGTTCCATCGAAAACATGAGGCTTAGTTGAAAACCTAGCAGCCATGGCAAAAACTCTAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.80% 30.20% 0.02% 0.00% NA
All Indica  2759 98.50% 1.40% 0.04% 0.00% NA
All Japonica  1512 11.90% 88.10% 0.00% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 98.80% 1.00% 0.17% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 2.00% 98.00% 0.00% 0.00% NA
Tropical Japonica  504 17.90% 82.10% 0.00% 0.00% NA
Japonica Intermediate  241 31.10% 68.90% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0413685186 A -> G LOC_Os04g23930.1 upstream_gene_variant ; 268.0bp to feature; MODIFIER silent_mutation Average:26.571; most accessible tissue: Minghui63 flag leaf, score: 43.614 N N N N
vg0413685186 A -> G LOC_Os04g23940.1 downstream_gene_variant ; 4796.0bp to feature; MODIFIER silent_mutation Average:26.571; most accessible tissue: Minghui63 flag leaf, score: 43.614 N N N N
vg0413685186 A -> G LOC_Os04g23920-LOC_Os04g23930 intergenic_region ; MODIFIER silent_mutation Average:26.571; most accessible tissue: Minghui63 flag leaf, score: 43.614 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0413685186 NA 4.11E-13 mr1010 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 NA 1.89E-21 mr1163 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 NA 1.82E-34 mr1350 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 NA 1.39E-20 mr1689 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 NA 7.79E-21 mr1698 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 NA 2.59E-20 mr1010_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 NA 2.62E-29 mr1350_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 3.10E-06 5.61E-11 mr1350_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 NA 2.70E-21 mr1698_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 6.36E-06 4.46E-19 mr1730_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 2.63E-09 1.74E-10 mr1730_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 NA 9.48E-16 mr1866_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413685186 3.44E-06 2.05E-06 mr1866_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251